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VarDetect

A sequence variation exploration tool



Software : Download. (Require J2RE 1.4 or later)

Tutorial  :  VarDetect Graphical User Interface (download) VarDetect command line (download)  (Require Flash player)

Samples Data :

The below are links to the data that published in:

Tocharoentanaphol C, Promso S, Zelenika D, Lowhnoo T, Tongsima S, Sura T, Chantratita W, Matsuda F, Mooney S, Sakuntabhai A.

"Evaluation of resequencing on number of tag SNPs of 13 atherosclerosis-related genes in Thai population". J Hum Genet. 2008;53(1):74-86

Gene CCL2
(2 contigs)
Trace files
XML Reference
Gene ITGAM
(13 contigs)
Trace files
XML Reference
Gene ITGAX
(15 contigs)
Trace files
XML Reference
Gene ITGB7
(9 contigs)
Trace files
XML Reference
Gene LIPG
(1 contig)
Trace files
XML Reference

 

Experimental results  :

 Gene Experimentally validated VarDetect results
No. of contig No. of SNP Detected TP FP FN Result view
 ACOX2 5 10 38 10 28 0 Ct1 Ct2 Ct3 Ct4 Ct5
 ADM 2 2 5 1 4 1 Ct1 Ct2
 ARRB1 6 16 21 15 6 1 Ct1 Ct2 Ct3 Ct4 Ct5 Ct6
 CACNA1D 11 26 30 23 7 3 Ct1 Ct2 Ct3 Ct4 Ct5 Ct6 Ct7 Ct8 Ct9 Ct10 Ct11
 CACNB3 3 8 7 5 2 3 Ct1 Ct2 Ct3
 CCL2 2 3 13 3 10 0 Ct1 Ct2
 CCL3 2 14 11 11 0 3 Ct1 Ct2
 CCL4 2 10 17 8 9 2 Ct1 Ct2
 CCL5 2 3 3 3 0 0 Ct1 Ct2
 CCR7 2 2 5 2 3 0 Ct1 Ct2
 ITGAM 13 39 40 29 11 10 Ct1 Ct2 Ct3 Ct4 Ct5 Ct6 Ct7 Ct8 Ct9 Ct10 Ct11 Ct12 Ct13
 ITGAX 15 25 52 24 28 1 Ct1 Ct2 Ct3 Ct4 Ct5 Ct6 Ct7 Ct8 Ct9 Ct10 Ct11 Ct12 Ct13 Ct14 Ct15
 ITGB7 9 19 26 16 10 3 Ct1 Ct2 Ct3 Ct4 Ct5 Ct6 Ct7 Ct8 Ct9
 LIPG 1 4 3 2 1 2 Ct1
 NPY 2 11 11 7 4 4 Ct1 Ct2

 Detected=Detected SNPs, TP=True positive, FP=False positive, FN=False negative

** To view the result files you must install the SVG viewer plugin on your browser. If you use Firefox or Opera browser, they have built-in SVG viewer, don't require installation.

If you use IE or Safari browser, you must install SVG viewer from Adobe by click here.

 

Comparison of the efficiency of VarDetect, PolyPhred, Genalys, novoSNP and Mutation Surveyor * :

Gene (contigs) Verified
SNPs
VarDetect PolyPhred Genalys novoSNP Mut.Surveyor
TP FP FN TP FP FN TP FP FN TP FP FN TP FP FN
 ACOX2 (5) 10 10 28 0 3 1 7 6 277 4 9 352 1 6 40 4
 ADM (2) 2 1 4 1 0 0 2 1 260 1 2 220 0 1 11 1
 ARRB1 (6) 16 15 7 1 9 1 7 16 30 0 15 58 1 13 13 3
 CACNA1D (11) 26 23 9 3 12 4 14 20 363 6 26 361 0 22 60 4
 CACNB3 (3) 6 5 4 1 4 1 2 5 191 1 5 308 1 3 51 3
 CCL2 (2) 3 3 10 0 1 0 2 3 196 0 3 130 0 2 34 1
 CCL3 (2) 12 11 4 1 4 0 8 9 171 3 12 123 0 9 31 3
 CCL4 (2) 10 8 11 2 6 3 4 8 136 2 8 96 2 7 20 3
 CCL5 (2) 3 3 2 0 3 1 0 3 28 0 3 21 0 2 3 1
 CCR7 (2) 2 2 3 0 1 0 1 2 75 0 2 129 0 1 3 1
 ITGAM (13) 27 19 20 8 17 7 10 19 552 8 23 618 4 22 63 5
 ITGAX (15) 25 24 28 1 13 4 12 22 704 3 24 1166 1 19 131 6
 ITGB7 (9) 16 15 13 1 11 1 5 15 435 1 16 521 0 11 32 5
 LIPG (1) 4 2 2 2 1 2 3 3 82 1 3 102 1 3 2 1
 NPY (2) 9 7 4 2 5 0 4 8 228 1 9 334 0 7 11 2
 Total 15 genes 77 contigs 171 148 149 23 90 25 81 140 3728 31 160 4539 11 128 505 43
 Precision 49.83 % 78.26 % 3.62 % 3.40 % 20.22 %
 Recall 86.55 % 52.63 % 81.87 % 93.57 % 74.85 %
 F-score 63.25 % 62.94 % 6.93 % 6.56 % 31.84 %

 

* We tested these experiments with using the default parameters of each tool. All tool use the SNP detection function only. Please see below for the details.

** Precision = TP/(TP + FP), Recall = TP/(TP + FN) and F-score = 2 * (Precision * Recall)/(Precision + Recall)

  • Default parameters setting
    • VarDetect
      • in Basecalling, set Noise Level to 7%, Heterozygous Level to 30%, Bin-Height to Static, Max Height to 1600 and Window Span to 5.
      • in Fast Alignment, set Window Quality to 90% and Window Size to 30 bases.
      • in SNP Detection, set Acceptable Quality to 90%, Vertical Quality to 90%, Differential Quality to 12.5% and SNP Detection Frequency to 3%.
    • PolyPhred
      • default quality threshold to trim sequence at the ends set to 25.
      • default SNPs score threshold set to 70 (PolyPhred detect as true SNPs only that have score 70-99).
    • Genalys
      • in Base-calling, set Mixture Cutoff to 20%, Peak Cutoff to 5%, Curvature Cutoff to 3% and N Average to 3.
      • in Homology setting, set Comparison unit size to 30 and %Homology for unit to 70% and Search Direction to Both Direction.
      • in Auto SNP Detection, set DNA Sample to Mixed and Number of Allele to 4.
    • novoSNP
      • in Add runs function, set Simple base qualities to Allways, set use Phred to As fallback and Quality clipping Cutoff to 0.02 (the higher cutoff, the less sequence is being clipped).
      • don't use Phred.
    • Mutation Survayor
      • in Alignment (Contig), set Fragment size (Sliding window) to 12 bp, Matching Base Number to 60 (if the number of bases that match between two sequences is greater than this setting (60 bp), they are mark as same contig) and Matching Base Percentage to 30%.
      • in Trimming, set Quality Trim to use phred score and set score to 15.
      • in Mutation Detection, set Mutation score to 5 and Mutation Height (the minimum mutation peak) to 500.

 

 

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